In silico analysis of putative transcription factor binding sites in the promoter region of drought responsive bZIP1 gene in rice and its orthologue in Arabidopsis thaliana
Abstract
The regulation of various biological processes in the plant systems, especially during different adverse climatic conditions are brought about by the change in the expression of different genes which in turn is the result of the binding of specific transcription factors in their respective transcription factor binding sites (TFBSs). In plants, basic region/leucine zipper motif (bZIP) transcription factors regulate processes including pathogen defense, light and stress signaling, seed maturation and flower development. In this study, an in silico analysis was done to predict the TFBSs for the bZIP1 gene of rice responses to drought. The AGI code of bZIP1 was utilized for the prediction of TFBSs by performing orthologue search against Arabidopsis genome in RGAP (Rice Genome Annotation Project) database. Further, TFBSs were identified by AthaMap database, a genome-wide map of TFBSs in Arabidopsis thaliana, and STIFDB2 (Stress Responsive Transcription Factor Database V2.0) database which is a comprehensive collection of biotic and abiotic stress responsive genes in Arabidopsis and Oryza sativa L. The significant TFBSs were analyzed based on the parameters provided by databases and were cross validated. The results revealed that the MYB, HSF and WRKY Transcription Factor families and their respective TFBSs were predicted as functionally significant. These predicted TFBSs would be responsible for the change in expression of bZIP1 gene under water stress. Such information will also help to understand the metabolic, physiological and cellular mechanisms implicated in such processes. These studies could help to engineer the plants for resistance to stress and achieve better yield in crop plants.Downloads
Additional Files
- Schematic pipeline of the computational workflow involved in TFBS prediction in drought responsive bZIP1 gene
- 1000bp TF map of bZIP1 gene obtained by STIFDB2 database
- Common TFs found in bZIP1 gene promoter; the transcription factors MYB, HSF, bZIP and WRKY were localized in both AthaMap and STIFDB2 databases
- Predicted TFBs on promoter region of bZIP1 gene using AthaMap database
- Predicted TFBSs identified for bZIP1 gene using STIFDB2 database
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